After having the ECU re-flashed on my 06 S4R (996 motor) the bike is surging a little at constant low RPM’s and it is backfiring/popping on decell. The bike never did this on the stock map even with the full Zard system: it runs great when out on the road and in the twistys. I have had the TPS reset and the fuel trim done. The dealer who did the re-flash said that I had to set the TPS manually to get rid of the issues. I have searched high and low on setting the TPS manually and I have found that it can be done and that it cannot be done. Is setting the TPS manually possible or should I return the ECU and have the dealer put a stock map back on the ECU?
I've read on the sport classic forum that guys have reset the tps manually by cycling their ignition on/off 5 times in a row and then starting the bike. I am skeptical of this, but it's worth a try in your case. I'd leave the kill switch off till the last cycle or you'll prime the motor with too much fuel too.